---
name: "fsa_ctg_bridge"
section: "1"
platform: "linux"
package: "mecat2"
version: "0.0+git20200428.f54c542+ds-4"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/fsa_ctg_bridge"
---

# fsa\_ctg\_bridge(1)

Bridge contigs

## NAME

fsa\_ctg\_bridge - Bridge contigs

## SYNOPSIS

**fsa\_ctg\_bridge** \[*options*\] *rawreads contigs read2ctg bridged\_contigs*

## DESCRIPTION

Command line tool to bridge contigs.

It takes the following parameters:

-

  rawreads

-

  	rawread file

-

  contigs

-

  	The contig file

-

  read2ctg

-

  	The file containing overlaps between rawread and contigs

-

  bridged\_contigs

-

  	The output file

## OPTIONS

**--ctg2ctg\_file**=*STRING*

-

  filename containing overlaps between contigs default: ""

**--read\_min\_length**=*INT*

-

  minimum rawread length default: 10000

**--ctg\_min\_length**=*INT*

-

  minimum contig length default: 500

**--read2ctg\_min\_identity**=*DOUBLE*

-

  minimum identity of overlaps between rawreads and contigs default: 80

**--ctg2ctg\_min\_identity**=*DOUBLE*

-

  minimum identity of overlaps between contigs default: 95

**--read2ctg\_max\_overhang**=*INT*

-

  maximum overhang of overlaps between rawreads and contigs default: 500

**--ctg2ctg\_max\_overhang**=*INT*

-

  maximum overhang of overlaps between contigs default: 100

**--read2ctg\_min\_aligned\_length**=*INT*

-

  minimum aligned length of overlaps between rawreads and contigs default: 5000

**--ctg2ctg\_min\_aligned\_length**=*INT*

-

  minimum aligned length of overlaps between contigs default: 2000

**--read2ctg\_min\_coverage**=*INT*

-

  minimum coverage of links between rawreads and contigs default: 4

**--min\_contig\_length**=*INT*

-

  minimum length of bridged contig default: 500

**--output\_directory**=*STRING*

-

  directory for output files default: "."

**--select\_branch=**"no\|best"

-

  selecting method when encountering branches in the graph, "no" = do not select any branch, "best" = select the most probable branch default: "no"

**--dump**

-

  for testing, dump intermediate files

**--thread\_size**=*INT*

-

  number of threads default: 4

Usage: fsa\_ctg\_bridge \[options\] rawreads contigs read2ctg bridged\_contigs

-

  rawreads

-

  rawread file

-

  contigs

-

  contig file

-

  read2ctg

-

  file containing overlaps between rawread and contigs

-

  bridged\_contigs

-

  output file

**--ctg2ctg\_file**=*STRING*

-

  filename containing overlaps between contigs default: ""

**--read\_min\_length**=*INT*

-

  minimum rawread length default: 10000

**--ctg\_min\_length**=*INT*

-

  minimum contig length default: 500

**--read2ctg\_min\_identity**=*DOUBLE*

-

  minimum identity of overlaps between rawreads and contigs default: 80

**--ctg2ctg\_min\_identity**=*DOUBLE*

-

  minimum identity of overlaps between contigs default: 95

**--read2ctg\_max\_overhang**=*INT*

-

  maximum overhang of overlaps between rawreads and contigs default: 500

**--ctg2ctg\_max\_overhang**=*INT*

-

  maximum overhang of overlaps between contigs default: 100

**--read2ctg\_min\_aligned\_length**=*INT*

-

  minimum aligned length of overlaps between rawreads and contigs default: 5000

**--ctg2ctg\_min\_aligned\_length**=*INT*

-

  minimum aligned length of overlaps between contigs default: 2000

**--read2ctg\_min\_coverage**=*INT*

-

  minimum coverage of links between rawreads and contigs default: 4

**--min\_contig\_length**=*INT*

-

  minimum length of bridged contig default: 500

**--output\_directory**=*STRING*

-

  directory for output files default: "."

**--select\_branch=**"no\|best"

-

  selecting method when encountering branches in the graph, "no" = do not select any branch, "best" = select the most probable branch default: "no"

**--dump**

-

  for testing, dump intermediate files

**--thread\_size**=*INT*

-

  number of threads default: 4